Starting phenix.real_space_refine on Sun Mar 10 18:01:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkf_14040/03_2024/7qkf_14040.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkf_14040/03_2024/7qkf_14040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkf_14040/03_2024/7qkf_14040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkf_14040/03_2024/7qkf_14040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkf_14040/03_2024/7qkf_14040.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkf_14040/03_2024/7qkf_14040.pdb" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 1164 2.51 5 N 336 2.21 5 O 351 1.98 5 H 1926 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3783 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 804 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "B" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 457 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 804 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "D" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 457 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "E" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 804 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "F" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 457 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Time building chain proxies: 2.22, per 1000 atoms: 0.59 Number of scatterers: 3783 At special positions: 0 Unit cell: (70.04, 91.464, 33.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 351 8.00 N 336 7.00 C 1164 6.00 H 1926 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS B 322 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS D 322 " distance=2.04 Simple disulfide: pdb=" SG CYS E 322 " - pdb=" SG CYS F 322 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 543.8 milliseconds 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 432 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.709A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 317 through 322 Processing sheet with id=AA3, first strand: chain 'C' and resid 325 through 330 Processing sheet with id=AA4, first strand: chain 'C' and resid 339 through 340 removed outlier: 6.791A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.255A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 349 through 350 removed outlier: 6.513A pdb=" N ARG A 349 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 353 through 356 removed outlier: 6.445A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.422A pdb=" N VAL B 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL D 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 313 through 324 removed outlier: 6.772A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N SER D 316 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B 315 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL D 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 328 through 329 removed outlier: 6.635A pdb=" N ILE B 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) 43 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.55 - 0.80: 3 0.80 - 1.06: 480 1.06 - 1.31: 1771 1.31 - 1.56: 1542 1.56 - 1.81: 14 Bond restraints: 3810 Sorted by residual: bond pdb=" CG2 VAL A 313 " pdb="HG23 VAL A 313 " ideal model delta sigma weight residual 0.970 0.553 0.417 2.00e-02 2.50e+03 4.35e+02 bond pdb=" CG2 VAL A 313 " pdb="HG21 VAL A 313 " ideal model delta sigma weight residual 0.970 0.586 0.384 2.00e-02 2.50e+03 3.68e+02 bond pdb=" CG2 VAL A 313 " pdb="HG22 VAL A 313 " ideal model delta sigma weight residual 0.970 0.727 0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" NH1 ARG A 349 " pdb="HH12 ARG A 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N SER E 324 " pdb=" H SER E 324 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 3805 not shown) Histogram of bond angle deviations from ideal: 70.15 - 82.65: 20 82.65 - 95.16: 13 95.16 - 107.66: 803 107.66 - 120.16: 5220 120.16 - 132.67: 895 Bond angle restraints: 6951 Sorted by residual: angle pdb=" CG1 VAL B 318 " pdb=" CB VAL B 318 " pdb=" HB VAL B 318 " ideal model delta sigma weight residual 108.00 70.15 37.85 3.00e+00 1.11e-01 1.59e+02 angle pdb=" CA VAL F 313 " pdb=" CB VAL F 313 " pdb=" CG1 VAL F 313 " ideal model delta sigma weight residual 110.40 130.74 -20.34 1.70e+00 3.46e-01 1.43e+02 angle pdb=" CA VAL B 318 " pdb=" CB VAL B 318 " pdb=" CG1 VAL B 318 " ideal model delta sigma weight residual 110.40 130.66 -20.26 1.70e+00 3.46e-01 1.42e+02 angle pdb=" CG1 VAL F 318 " pdb=" CB VAL F 318 " pdb=" HB VAL F 318 " ideal model delta sigma weight residual 108.00 72.50 35.50 3.00e+00 1.11e-01 1.40e+02 angle pdb=" CA VAL B 318 " pdb=" CB VAL B 318 " pdb=" HB VAL B 318 " ideal model delta sigma weight residual 109.00 75.33 33.67 3.00e+00 1.11e-01 1.26e+02 ... (remaining 6946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 1576 17.80 - 35.59: 106 35.59 - 53.39: 42 53.39 - 71.18: 42 71.18 - 88.98: 4 Dihedral angle restraints: 1770 sinusoidal: 1014 harmonic: 756 Sorted by residual: dihedral pdb=" C VAL A 337 " pdb=" N VAL A 337 " pdb=" CA VAL A 337 " pdb=" CB VAL A 337 " ideal model delta harmonic sigma weight residual -122.00 -137.87 15.87 0 2.50e+00 1.60e-01 4.03e+01 dihedral pdb=" CA LYS B 317 " pdb=" C LYS B 317 " pdb=" N VAL B 318 " pdb=" CA VAL B 318 " ideal model delta harmonic sigma weight residual 180.00 152.18 27.82 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA GLY A 334 " pdb=" C GLY A 334 " pdb=" N GLY A 335 " pdb=" CA GLY A 335 " ideal model delta harmonic sigma weight residual 180.00 152.25 27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 1767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 262 0.231 - 0.462: 13 0.462 - 0.694: 2 0.694 - 0.925: 3 0.925 - 1.156: 5 Chirality restraints: 285 Sorted by residual: chirality pdb=" CB VAL D 318 " pdb=" CA VAL D 318 " pdb=" CG1 VAL D 318 " pdb=" CG2 VAL D 318 " both_signs ideal model delta sigma weight residual False -2.63 -1.47 -1.16 2.00e-01 2.50e+01 3.34e+01 chirality pdb=" CB VAL E 313 " pdb=" CA VAL E 313 " pdb=" CG1 VAL E 313 " pdb=" CG2 VAL E 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.50 -1.13 2.00e-01 2.50e+01 3.17e+01 chirality pdb=" CB VAL D 313 " pdb=" CA VAL D 313 " pdb=" CG1 VAL D 313 " pdb=" CG2 VAL D 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.55 -1.08 2.00e-01 2.50e+01 2.90e+01 ... (remaining 282 not shown) Planarity restraints: 549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 307 " 0.048 2.00e-02 2.50e+03 4.78e-02 3.42e+01 pdb=" CD GLN B 307 " -0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN B 307 " -0.046 2.00e-02 2.50e+03 pdb=" NE2 GLN B 307 " 0.025 2.00e-02 2.50e+03 pdb="HE21 GLN B 307 " -0.069 2.00e-02 2.50e+03 pdb="HE22 GLN B 307 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 330 " 0.054 2.00e-02 2.50e+03 3.89e-02 3.41e+01 pdb=" CG HIS E 330 " -0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS E 330 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS E 330 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 HIS E 330 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS E 330 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 HIS E 330 " 0.028 2.00e-02 2.50e+03 pdb=" HE1 HIS E 330 " 0.043 2.00e-02 2.50e+03 pdb=" HE2 HIS E 330 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 333 " 0.032 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" N GLY A 334 " -0.098 2.00e-02 2.50e+03 pdb=" CA GLY A 334 " 0.029 2.00e-02 2.50e+03 pdb=" H GLY A 334 " 0.038 2.00e-02 2.50e+03 ... (remaining 546 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 421 2.23 - 2.82: 7031 2.82 - 3.42: 10020 3.42 - 4.01: 13175 4.01 - 4.60: 18482 Nonbonded interactions: 49129 Sorted by model distance: nonbonded pdb=" HG SER A 356 " pdb=" OD1 ASP C 358 " model vdw 1.640 1.850 nonbonded pdb=" OD1 ASP A 358 " pdb=" HG SER E 356 " model vdw 1.653 1.850 nonbonded pdb=" HZ2 LYS A 331 " pdb=" OD1 ASP F 314 " model vdw 1.684 1.850 nonbonded pdb=" HG SER A 316 " pdb=" O SER C 316 " model vdw 1.717 1.850 nonbonded pdb=" OD2 ASP B 314 " pdb=" HZ2 LYS C 331 " model vdw 1.725 1.850 ... (remaining 49124 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 11.450 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.310 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.136 1884 Z= 0.824 Angle : 2.232 20.336 2520 Z= 1.446 Chirality : 0.205 1.156 285 Planarity : 0.010 0.033 318 Dihedral : 13.419 88.978 717 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 0.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.93 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.44), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.33), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.004 HIS D 330 PHE 0.013 0.003 PHE C 346 TYR 0.035 0.009 TYR C 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 311 LYS cc_start: 0.6624 (mtpt) cc_final: 0.6148 (mttm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 2.4533 time to fit residues: 174.6247 Evaluate side-chains 38 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN C 336 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 1884 Z= 0.326 Angle : 1.121 10.638 2520 Z= 0.573 Chirality : 0.246 1.410 285 Planarity : 0.005 0.035 318 Dihedral : 7.935 25.321 252 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.31 % Allowed : 14.81 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.39), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.30), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 330 PHE 0.002 0.001 PHE E 346 TYR 0.013 0.002 TYR A 310 ARG 0.002 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 311 LYS cc_start: 0.6498 (mtpt) cc_final: 0.6137 (mttp) REVERT: E 353 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8424 (mtpp) outliers start: 5 outliers final: 2 residues processed: 43 average time/residue: 2.6453 time to fit residues: 115.7261 Evaluate side-chains 40 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 353 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS A 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1884 Z= 0.258 Angle : 1.073 10.788 2520 Z= 0.543 Chirality : 0.254 1.433 285 Planarity : 0.005 0.038 318 Dihedral : 6.834 22.394 252 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.31 % Allowed : 17.13 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.38), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.29), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.005 0.001 PHE E 346 TYR 0.008 0.001 TYR A 310 ARG 0.003 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 311 LYS cc_start: 0.6224 (mtpt) cc_final: 0.5893 (mttp) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 2.5070 time to fit residues: 104.7456 Evaluate side-chains 40 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 352 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1884 Z= 0.258 Angle : 1.058 10.945 2520 Z= 0.532 Chirality : 0.254 1.426 285 Planarity : 0.005 0.037 318 Dihedral : 6.404 20.624 252 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.78 % Allowed : 19.44 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.38), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.29), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.006 0.001 PHE E 346 TYR 0.010 0.001 TYR A 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 311 LYS cc_start: 0.6314 (mtpt) cc_final: 0.5975 (mttp) outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 2.3282 time to fit residues: 95.0288 Evaluate side-chains 38 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 352 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1884 Z= 0.256 Angle : 1.045 10.920 2520 Z= 0.528 Chirality : 0.255 1.425 285 Planarity : 0.005 0.037 318 Dihedral : 6.240 22.658 252 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.85 % Allowed : 18.06 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.38), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.29), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.006 0.001 PHE E 346 TYR 0.009 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 311 LYS cc_start: 0.6270 (mtpt) cc_final: 0.5948 (mttp) outliers start: 4 outliers final: 4 residues processed: 38 average time/residue: 2.2779 time to fit residues: 88.3056 Evaluate side-chains 38 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1884 Z= 0.243 Angle : 1.030 10.931 2520 Z= 0.522 Chirality : 0.255 1.426 285 Planarity : 0.005 0.039 318 Dihedral : 5.954 20.062 252 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.78 % Allowed : 16.20 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.38), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.29), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 330 PHE 0.005 0.001 PHE A 346 TYR 0.009 0.001 TYR A 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 311 LYS cc_start: 0.6188 (mtpt) cc_final: 0.5815 (mttp) outliers start: 6 outliers final: 5 residues processed: 38 average time/residue: 2.2589 time to fit residues: 87.6275 Evaluate side-chains 38 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 314 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1884 Z= 0.234 Angle : 1.022 10.953 2520 Z= 0.518 Chirality : 0.255 1.427 285 Planarity : 0.005 0.039 318 Dihedral : 5.773 19.951 252 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.24 % Allowed : 16.20 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.38), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.29), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 330 PHE 0.005 0.001 PHE A 346 TYR 0.009 0.001 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 311 LYS cc_start: 0.6129 (mtpt) cc_final: 0.5797 (mttp) outliers start: 7 outliers final: 5 residues processed: 40 average time/residue: 2.0663 time to fit residues: 84.5587 Evaluate side-chains 38 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 314 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1884 Z= 0.232 Angle : 1.019 10.912 2520 Z= 0.516 Chirality : 0.255 1.430 285 Planarity : 0.005 0.038 318 Dihedral : 5.633 19.208 252 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.31 % Allowed : 18.06 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.39), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.30), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 330 PHE 0.005 0.001 PHE E 346 TYR 0.009 0.001 TYR C 310 ARG 0.001 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 311 LYS cc_start: 0.6149 (mtpt) cc_final: 0.5774 (mttp) outliers start: 5 outliers final: 5 residues processed: 37 average time/residue: 2.1316 time to fit residues: 80.6993 Evaluate side-chains 38 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 341 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1884 Z= 0.233 Angle : 1.023 10.925 2520 Z= 0.517 Chirality : 0.254 1.426 285 Planarity : 0.005 0.038 318 Dihedral : 5.580 19.342 252 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.78 % Allowed : 18.06 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.39), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.30), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 330 PHE 0.005 0.001 PHE E 346 TYR 0.009 0.001 TYR C 310 ARG 0.001 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 311 LYS cc_start: 0.6114 (mtpt) cc_final: 0.5746 (mttp) outliers start: 6 outliers final: 6 residues processed: 37 average time/residue: 2.1546 time to fit residues: 81.4420 Evaluate side-chains 41 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 0.0370 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1884 Z= 0.231 Angle : 1.017 10.902 2520 Z= 0.515 Chirality : 0.254 1.418 285 Planarity : 0.005 0.038 318 Dihedral : 5.564 19.290 252 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.78 % Allowed : 18.98 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.39), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.30), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 330 PHE 0.005 0.001 PHE E 346 TYR 0.009 0.001 TYR C 310 ARG 0.001 0.000 ARG E 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 311 LYS cc_start: 0.6103 (mtpt) cc_final: 0.5738 (mttp) outliers start: 6 outliers final: 6 residues processed: 35 average time/residue: 2.1640 time to fit residues: 77.4662 Evaluate side-chains 39 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 0.0570 chunk 19 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.130694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.118564 restraints weight = 6473.510| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.75 r_work: 0.3771 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1884 Z= 0.228 Angle : 1.018 10.921 2520 Z= 0.515 Chirality : 0.255 1.423 285 Planarity : 0.005 0.038 318 Dihedral : 5.468 18.963 252 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.78 % Allowed : 20.37 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.40), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.30), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 330 PHE 0.004 0.001 PHE E 346 TYR 0.009 0.001 TYR C 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3277.55 seconds wall clock time: 57 minutes 44.15 seconds (3464.15 seconds total)